Contacts of the strand formed by residues 180 - 193 (chain D) in PDB entry 3IML
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D TYR* 3.3 4.8 - - - -
177D VAL* 2.9 35.8 + - + +
178D ASP* 3.2 6.2 + - + +
179D GLY* 1.3 78.0 - - - +
181D PRO* 1.3 75.8 - - + +
182D HIS 3.4 0.2 + - - -
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Residues in contact with PRO 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D GLU* 3.7 34.1 - - + +
140D LEU* 3.8 27.8 - - + -
174D VAL* 4.4 3.8 - - + -
175D ARG 3.9 5.6 - - - +
176D TYR* 3.7 21.8 - - + -
177D VAL* 5.2 0.7 - - - +
179D GLY 4.4 0.9 - - - +
180D LYS* 1.3 89.5 - - + +
182D HIS* 1.3 58.5 + - - +
219D LEU* 3.9 12.8 - - + +
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Residues in contact with HIS 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ARG* 2.9 51.9 + - - +
177D VAL* 3.4 36.6 - - + +
180D LYS 3.4 0.2 + - - -
181D PRO* 1.3 71.5 - - - +
183D SER* 1.3 71.0 + - - +
218D ASP 4.4 3.6 - - - +
219D LEU* 3.1 20.5 - - - +
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Residues in contact with SER 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D VAL* 3.7 5.4 - - - +
175D ARG* 2.8 48.1 + - - +
182D HIS* 1.3 91.6 + - - +
184D ILE* 1.3 68.2 + - - +
185D ASP* 4.4 1.0 + - - -
219D LEU* 3.3 16.0 - - - +
221D LYS* 4.5 18.4 - - - -
223D ASP* 4.2 11.7 + - - -
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 4.0 21.3 - - + -
172D VAL* 4.3 7.2 - - + -
173D THR 3.9 9.2 - - - +
174D VAL* 4.6 7.2 - - + +
183D SER* 1.3 74.1 - - - +
185D ASP* 1.3 63.1 + - - +
186D THR 4.1 4.5 - - - +
187D VAL* 3.7 28.5 - - + -
215D LEU* 3.5 32.3 - - + -
216D PRO* 4.3 5.6 - - + +
219D LEU* 2.9 42.1 + - + +
220D ILE* 5.0 0.2 - - + -
221D LYS 5.4 0.5 + - - -
223D ASP* 4.2 4.0 - - - +
224D ILE* 3.4 31.4 - - + +
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Residues in contact with ASP 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C THR 4.4 4.9 - - - +
6D LEU* 4.0 36.3 - - + +
173D THR* 2.9 23.3 + - + +
175D ARG* 4.8 4.5 - - + +
183D SER* 3.6 4.9 + - - +
184D ILE* 1.3 73.0 - - - +
186D THR* 1.3 78.6 + - - +
223D ASP* 3.7 15.6 - - - +
224D ILE* 3.7 1.4 - - - -
225D LYS* 3.0 54.2 + - - +
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Residues in contact with THR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C THR* 4.1 14.8 + - - +
171D GLN 3.8 0.4 - - - +
172D VAL* 3.5 2.9 - - - -
173D THR* 2.9 38.1 + - - +
184D ILE* 4.1 2.7 - - - +
185D ASP* 1.3 96.2 + - - +
187D VAL* 1.3 77.3 + - - +
188D VAL* 4.1 8.3 - - + -
225D LYS* 3.4 24.9 + - + +
227D LEU* 3.9 26.0 - - + -
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Residues in contact with VAL 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LEU* 3.5 27.8 - - + -
171D GLN 3.4 4.5 - - - +
172D VAL* 4.6 8.3 - - + -
184D ILE* 3.7 20.2 - - + -
186D THR* 1.3 80.3 - - - +
188D VAL* 1.3 69.0 + - - +
189D LEU* 4.1 0.6 + - + -
211D ILE* 3.9 36.4 - - + +
215D LEU* 4.4 13.7 - - + -
224D ILE* 5.0 0.4 - - + +
225D LYS 3.1 7.5 + - - +
226D PHE* 3.6 11.3 - - + +
227D LEU 2.9 24.8 + - - +
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Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLN* 3.9 17.7 - - + +
305C ALA* 4.2 14.8 - - + -
306C ILE* 5.0 5.8 - - + -
312C THR* 5.5 0.4 - - - +
170D SER* 3.3 5.5 - - - -
171D GLN* 2.7 54.1 + - + +
186D THR* 4.1 7.2 - - + -
187D VAL* 1.3 79.5 - - - +
189D LEU* 1.3 70.8 + - - +
190D SER* 4.6 4.9 - - - +
227D LEU* 3.2 32.8 - - + +
230D PRO* 4.7 13.2 - - + -
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Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LEU* 4.5 18.6 - - + +
149D VAL* 5.5 2.2 - - + +
152D GLN* 5.4 5.2 - - + -
168D ALA* 5.3 3.8 - - + -
169D LYS 3.5 8.3 - - - +
170D SER* 5.1 2.0 - - - -
187D VAL* 4.1 0.8 + - + -
188D VAL* 1.3 76.5 - - - +
190D SER* 1.3 73.5 + - - +
191D THR* 4.1 14.4 - - + +
206D VAL* 3.4 24.2 - - + -
210D VAL* 3.3 33.4 - - + -
211D ILE* 4.0 23.8 - - + -
227D LEU 2.7 10.8 + - - +
228D VAL* 3.1 8.6 - - + +
229D ASN 2.9 20.1 + - - -
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Residues in contact with SER 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLN* 5.5 1.5 + - - -
306C ILE* 4.1 14.4 - - - +
168D ALA* 3.1 5.4 - - - +
169D LYS* 2.8 48.6 + - - +
188D VAL* 4.6 4.5 - - - +
189D LEU* 1.3 72.1 - - - +
191D THR* 1.3 60.2 + - - +
229D ASN* 3.4 8.0 - - - -
230D PRO* 3.8 20.8 - - - +
231D THR* 5.5 1.0 + - - -
234D PHE* 4.2 16.7 - - - -
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D GLN* 2.9 27.9 + - - -
163D TRP* 5.0 0.2 - - + -
164D LEU* 3.2 17.8 - - + +
167D ASP 3.8 3.1 - - - -
168D ALA* 3.9 1.6 - - - -
189D LEU* 4.1 11.2 - - + -
190D SER* 1.3 73.6 - - - +
192D GLN* 1.3 73.8 + - - +
193D HIS* 3.5 3.6 - - - -
202D LEU* 4.2 16.6 - - + -
206D VAL* 4.3 15.5 - - + -
229D ASN* 2.9 39.1 + - - +
234D PHE* 3.3 7.4 - - - -
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Residues in contact with GLN 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TYR* 3.6 10.6 + - - -
164D LEU* 3.9 1.2 - - - -
165D ARG* 2.9 37.7 + - + +
166D PRO* 3.5 8.2 - - - +
167D ASP* 2.9 47.9 + - + +
191D THR* 1.3 86.9 + - - +
193D HIS* 1.3 64.3 + - - +
234D PHE* 3.1 24.1 - - + +
235D VAL 3.2 16.3 + - - +
236D ILE* 4.0 0.8 - - - +
237D GLY* 3.1 33.3 + - - +
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Residues in contact with HIS 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D TRP* 3.0 20.9 - - + +
165D ARG* 3.4 16.3 + - - +
191D THR 3.5 13.5 - - - -
192D GLN* 1.3 77.5 - - - +
194D ALA* 1.3 87.1 + - - +
195D PRO* 5.0 1.3 - - + -
197D ILE* 3.7 17.0 - - + +
199D LEU* 4.7 7.2 - - + +
202D LEU* 3.6 28.6 - - + +
229D ASN* 3.8 5.5 + - - -
233D ARG* 3.9 9.5 - - + -
234D PHE 2.9 42.0 + - - -
235D VAL* 3.4 32.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il